Output Files

Here, we will describe the output files of many SimNIBS see File Formats in SimNIBS for a detailed description of each file type

Head Segmentation

Both headreco and mri2mesh generate the same type of output

  • <sub_id>.msh

    Gmsh mesh file with head segmentation

  • m2m_<sub_id>/

    Folder with secondary output of the head segmentation process

Simulations

The final simulation results are in the Output Folder, which can be set in the GUI or in scripts. By default, this folder is called simnibs_simulation/, and is located in the same folder as the mesh file.

Below, we have:

TDCS

  • <sub_id>_TDCS_<poslist_nr>_<cond_type>.msh

    Gmsh mesh file with tDCS simulation results

  • <sub_id>_TDCS_<poslist_nr>_el_currents.geo

    Gmsh .geo file with simplified tDCS electrode models for visualization

TMS

  • <sub_id>_TMS_<poslist_nr>-<position_nr>_<coil_name>_<cond_type>.msh

    Gmsh mesh file with TMS simulation results

  • <sub_id>_TMS_<poslist_nr>-<position_nr>_<coil_name>_coil_pos.geo

    Gmsh .geo file with a simplified coil model showing it’s center and axes. For .ccd coil models, this is a more detail model showing dipoles.

Others

  • simnibs_simulation_yyyymmdd.log

    Simulation log

  • simnibs_simulation_yyyymmdd.mat

    Simulation configuration file, can be used to re-run the simulation

  • fields_summary.txt

    A few summary quantities for each field

Post-Processing

In the section below, we will use

  • For tDCS simulations:

    <simulation_name>=TDCS_<poslist_nr>_<cond_type>

  • For TMS simulations:

    <simulation_name>=TMS_<poslist_nr>-<position_nr>_<coil_name>_<cond_type>

Surface Mapping

  • subject_overlays/

    Surface overlays with fields in the subject specific space. Generated if the Interpolate to cortical surface (GUI) or the map_to_surf (script) are set

  • fsavg_overlays/

    Surface overlays with fields in FsAverage space. Generated if the Interpolate to FsAverage surface (GUI) or the map_to_fsavg (script) are set

Inside the folders, we have

  • <sub_id>_<simulation_name>_<central/fsavg>.msh

    Transformed result as a Gmsh .msh file for easy visualization

  • <lh/rh>_<simulation_name>.<central/fsavg>.<field>.<quantity>

    FreeSurfer generic overlay with given quantity (such as norm or normal) related to a given field.

Volume Mapping

  • subject_volumes/

    NIfTI volumes with fields in a subject specific space. Generated if Interpolate to a nifiti volume (GUI) or map_to_vol (scripts) are set.

  • mni_volumes/

    NIfTI volumes with fields in MNI space. Generated if Transform to MNI space (GUI) or map_to_mni (scripts) are set.

Inside the folders, we have NIfTI files with the field values. For vector fields such as E and J, the NIfTI files are composed of 3 volumes, each corresponding to a direction